For reference, most of the accepted answer is unnecessary. The only key part is this (in the UIViewController - no need to edit or subclass EAGLView / GLKView):
self.view.opaque = NO; // NB: Apple DELETES THIS VALUE FROM NIB
self.view.backgroundColor = [UIColor clearColor]; // Optional: you can do this in NIB instead
You can set the background Color in the NIB - but you CANNOT set the opacity (Apple seems to overwrite this var for GL views at initWithCoder :( )
Plus, of course, in your OpenGL code you need to clear to alpha=0.0. So, wherever your glClear / glClearColor calls are already, replace the clearColor with:
glClearColor( 0, 0, 0, 0.0);
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
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